A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly
Brittany Lott, Yongmei Wang, Takuya Nakazato
BMC Biophysics 2013, 6:13 (23 October 2013)
Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies
Anke Steinbach, Christine K Maurer, Elisabeth Weidel, Claudia Henn, Christian Brengel, Rolf W Hartmann, Matthias Negri
BMC Biophysics 2013, 6:10 (1 August 2013)
Enzyme kinetic analysis and surface plasmon resonance confirm the ping-pong mechanism of the enzyme PqsD in the biosynthesis of HHQ, a signaling molecule involved in quorum-sensing among the opportunistic pathogen
P seudomonas aeruginosa
Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations
Haina Qin, Liangzhong Lim, Jianxing Song
BMC Biophysics 2012, 5:2 (25 January 2012)
Structural determination of the EphA4 ligand binding domain provides the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity.
An upper limit for macromolecular crowding effects
Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak
BMC Biophysics 2011, 4:13 (31 May 2011)
Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics
Yu-ming M Huang, Chia-en A Chang
BMC Biophysics 2011, 4:12 (25 May 2011)
Mechanism of phosphothreonine/serine recognition and specificity is elucidated for three well-known phosphopeptide-binding domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated domain (FHA) with the use of molecular dynamics simulations.
Diffusion of hydrophobin proteins in solution and interactions with a graphite surface
Paolo Mereghetti, Rebecca C Wade
BMC Biophysics 2011, 4:9 (21 April 2011)
Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.
Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package
BMC Biophysics 2011, 4:7 (13 April 2011)
A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.
Gated Diffusion-controlled Reactions
J Andrew McCammon
BMC Biophysics 2011, 4:4 (2 March 2011)
Andy McCammon discusses both the protein-centric and detailed dynamic simulation methods that have been applied to predict rates of ligand binding and reactivity at protein active sites and the biological implications of these findings.
Diffusion in crowded biological environments: applications of Brownian dynamics
Maciej Długosz, Joanna Trylska
BMC Biophysics 2011, 4:3 (2 March 2011)
Maciej Dlugosz and Joanna Trylska review recent developments in particle-based Brownian dynamics algorithms and their application to model diffusive transport in crowded systems, which are proving useful in improving our understanding of metabolism, transport and signaling.